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- PDB-1qlt: STRUCTURE OF THE H422A MUTANT OF THE FLAVOENZYME VANILLYL-ALCOHOL... -

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Basic information

Entry
Database: PDB / ID: 1qlt
TitleSTRUCTURE OF THE H422A MUTANT OF THE FLAVOENZYME VANILLYL-ALCOHOL OXIDASE
ComponentsVANILLYL-ALCOHOL OXIDASE
KeywordsFLAVOENZYME / OXIDOREDUCTASE / FLAVOPROTEIN / METHANOL UTILIZATION / PEROXISOME / OXIDASE / CATALYSIS
Function / homology
Function and homology information


vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / methanol metabolic process / lactate catabolic process / D-lactate dehydrogenase (cytochrome) activity / D-lactate dehydrogenase (NAD+) activity / FAD binding / peroxisome / mitochondrion
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidases, C-terminal domain / FAD-linked oxidase, C-terminal / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 ...Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidases, C-terminal domain / FAD-linked oxidase, C-terminal / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / Vanillyl-alcohol oxidase
Similarity search - Component
Biological speciesPENICILLIUM SIMPLICISSIMUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsMattevi, A. / Fraaije, M.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Covalent flavinylation is essential for efficient redox catalysis in vanillyl-alcohol oxidase.
Authors: Fraaije, M.W. / van den Heuvel, R.H. / van Berkel, W.J. / Mattevi, A.
#1: Journal: Proteins: Struct.,Funct., Genet. / Year: 1997
Title: Crystallization and Preliminary X-Ray Analysis of the Flavoenzyme Vanillyl-Alcohol Oxidase from Penicillium Simplicissimum
Authors: Mattevi, A. / Fraaije, M.W. / Coda, A. / Van Berkel, W.J.
History
DepositionSep 16, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Experimental preparation
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / reflns
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _exptl_crystal_grow.method / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VANILLYL-ALCOHOL OXIDASE
B: VANILLYL-ALCOHOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,5696
Polymers125,8802
Non-polymers1,6894
Water6,702372
1
A: VANILLYL-ALCOHOL OXIDASE
B: VANILLYL-ALCOHOL OXIDASE
hetero molecules

A: VANILLYL-ALCOHOL OXIDASE
B: VANILLYL-ALCOHOL OXIDASE
hetero molecules

A: VANILLYL-ALCOHOL OXIDASE
B: VANILLYL-ALCOHOL OXIDASE
hetero molecules

A: VANILLYL-ALCOHOL OXIDASE
B: VANILLYL-ALCOHOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)510,27624
Polymers503,5198
Non-polymers6,75716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area48890 Å2
ΔGint-410.4 kcal/mol
Surface area168820 Å2
MethodPQS
Unit cell
Length a, b, c (Å)129.660, 129.660, 132.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.232426, -0.972447, 0.018018), (-0.972521, -0.23262, -0.00955), (0.013478, -0.015304, -0.999792)
Vector: 111.842, 143.493, 111.349)
DetailsBIOLOGICAL_UNIT: OCTAMER

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Components

#1: Protein VANILLYL-ALCOHOL OXIDASE / ARYL-ALCOHOL OXIDASE / 4-ALLYLPHENOL OXIDASE


Mass: 62939.910 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PENICILLIUM SIMPLICISSIMUM (fungus) / Description: FUNGUS / Cellular location: INTRACELLULAR / Organelle: PEROXISOMES / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P56216, aryl-alcohol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 40 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6 / Details: FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Details: Mattevi, A., (1997) Proteins: Struct.,Funct., Genet., 27, 601.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 mg/mlenzyme1drop
225 mMsodium phosphate1drop
350 mMsodium acetate1drop
40.01 %(w/v)1dropNaN3
53 %(w/v)PEG40001drop
6100 mMsodium acetate1reservoir
70.02 %(w/v)1reservoirNaN3
86 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 55414 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.226 / % possible all: 78.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 285553
Reflection shell
*PLUS
% possible obs: 78.8 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2000 4 %RANDOM
Rwork0.21 ---
obs0.212 55414 93.1 %-
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8692 0 114 372 9178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_planar_d0.023
X-RAY DIFFRACTIONp_plane_restr0.011

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